added check for missing file in SeqIO

Author: lynnjo

src/main/kotlin/biokotlin/seqIO/SeqIO.kt

@@ -61,6 +61,7 @@ private fun seqIterator(format: SeqFormat, type: SeqType, filename: String): Seq
 fun reader(filename: String, format: SeqFormat? = null, type: SeqType = SeqType.nucleotide): SequenceIterator {
 
     assert(filename.isNotEmpty())
+    require(File(filename).exists()) { "File not found: $filename"}
 
     val formatToUse = if (format != null) {
         format

src/test/kotlin/biokotlin/seqIO/FastaIOTest.kt

@@ -4,6 +4,7 @@ import biokotlin.seq.*
 import biokotlin.util.bufferedReader
 import io.kotest.core.spec.style.StringSpec
 import io.kotest.matchers.shouldBe
+import org.junit.jupiter.api.assertThrows
 import java.io.File
 
 class FastaIOTest : StringSpec({
@@ -18,6 +19,14 @@ class FastaIOTest : StringSpec({
             "B73V4_ctg58" to 196,
             "B73V4_ctg43" to 161
     )
+    "Verify file exists" {
+        // this test verifies that when given a non-existing file, the exception is propagated
+        // and the test does not hang
+        val badFile = "/Users/lcj34/debug/biokotlin/nonExisting.fa"
+        assertThrows<IllegalArgumentException>{
+            NucSeqIO(badFile)
+        }
+    }
 
     "iterateFile" {